Chapter 3 - Biological Molecules Flashcards
Why is water polar?
Unequal electron distribution between O-H bonds creating dipoles
Properties of Water
Water is cohesive meaning it moves as one mass, allowing plants to take water up from the roots.
Water acts as a coolant which allows organisms to cool down and remain at optimal temperatures
Water is a polar solvent meaning it is a good solvent where organisms can be dissolved
Water is stable because it has a high specific heat capacitytakes a lot of energy for it to change temperature.
Ice is less dense than water because the hydrogen bonds fix the molecules further apart from each other in the solid state and freeze them in place. Molecules in solid state are frozen further apart from each other than the molecules in the liquid state
Carbohydrates
Molecules that contain only carbon, hydrogen and oxygen. Known as saccharides or sugars
Monosaccharides
Glucose, Fructose and Ribose
Single sugar
Disaccharides (examples)
When two monosaccharides join together through glycosidic bonds and a condensation reaction.
Examples of Disaccharides are Lactose and Sucrose
Polysaccharides (Examples)
When multiple monosaccharides join together to form a polysaccharide.
Cellulose and Starch
Alpha Glucose and Beta Glucose
Alpha glucose has a OH group below
Beta glucose has a OH group above
Condensation reactions
These are the reactions that happen when two monosaccharides join together through glycosidic bonds and water is produced. In two glucose monomers that join together, it is a C1 to C4 bond
Peptide, Glycosidic and Phosphodiester bonds are all formed through condensation reactions
Starch
Store of glucose in plants
This is a polysaccharide. Made when alpha glucose molecules join together through glycosidic bonds.
There are two different polysaccharides that form starch. They are called Amylose and Amylopectin
Amylose
A component of starch. These have carbon 1-4 bonds. These are between alpha glucose molecules and the bond angle between these aswell as the hydrogen bonds between this polysaccharide chain. The glycosidic bond and the hydrogen bonds make the polysaccharide arrange into a helix structure. Structure is very compact due to the hydrogen bonds and the glycosidic bonds making amylose less soluble in water
Amylopectin
This is a second type of starch. This is between 1-4 alpha glucose molecules. But there are also carbon 1-6 glycosidic bonds which create branches from the polysaccharide chain.
Amylopectin like amylose is very compact and therefore insoluble in water which makes it suitable for storage.
The branching of the glycosidic chains means there are areas in which free glucose molecules are able to be added but also broken off. Speeds up the process of releasing energy
Cellulose
This is what the cell wall in plants is made up of (structural support)
Composed of alternate rotations (180) of beta glucose molecules joined together. Because OH groups are too far from each other
The 3D shape is straight chained molecules.
Cellulose molecules form hydrogen bonds with other cellulose molecules which are called microfibrils
Many microfibrils form macrofibrils which are strong and insoluble, making them suitable to compose the cell wall
Microfibrils
When molecules of cellulose form hydrogen bonds with each other. These then from macro-fibrils which are strong and insoluble which make them suitable to make up the cell wall.
Lipids
Lipids are fats and oils and used as a source of energy, composed of Carbon hydrogen and oxygen just like carbohydrates.
They are non polar molecules
They are macromolecules meaning they are made up of repeating units
Triglyceride
A triglyceride is a molecule made up of one glycerol molecule and three fatty acid chains.
Joined together through ester bonds between each of the fatty acids.
Saturated fatty acids
- Have no carbon to carbon double bonds
- Molecules can therefore be packed close together and exist in a solid state
Unsaturated fatty acids
- Have a carbon double bond which creates kinks in the structure.
- Molecules can therefore not pack close together and exist in the liquid state (oil)
Phospholipids
- Made up of a glycerol molecule, two fatty acids and a phosphate ion.
- Hydrophobic fatty acid tails because it is non polar
- Hydrophillic phosphate head because it is polar (ion)
Roles of lipids
- Hormone production
- Waterproofing (waxy cuticle)
- Thermal insulation
- Cushioning, protects vital organs like the heart and kidneys
Lipid test
- Emulsion test where the sample is mixed with ethanol and then added to water
- If a white emulsion layer appears at the top, the test is positive
- If the reading of the solution remains clear, the test is negative
Lipid test
- Emulsion test where the sample is mixed with ethanol and then added to water
- If a white emulsion layer appears at the top, the test is positive
- If the reading of the solution remains clear, the test is negative
Proteins
- Made from amino acids (protein monomers)
- Amino acids make up peptides which are chains of amino acids joined together
- Carbon, Hydrogen, Oxygen and Nitrogen
How do amino acids join together
- On either side of an amino acid, there is an amine (NH2) group and a carboxylic acid group.
- A condensation reaction undergoes this and forms a peptide bond between each amino acid and water is produced
- When they join together, they form a polypeptide (dipeptides, tripeptides, Oligopeptides)
- These polypeptides interact and form structures like proteins
Primary Structure (Proteins)
- The sequence in which amino acids are joined together.
- DNA controls the way in which amino acids join together.
- The only bonds present in this stage are peptide bonds
Secondary Structure (Proteins)
- Hydrogen bonding between the polypeptide chains.
- Forms the secondary structure which is either alpha helixes or beta-pleated sheets.
Tertiary Structure
The folding of a protein into its final shape. R-group interactions cause further folding
They have R-group interactions between different amino acids because the secondary structure brings amino acids closer together.
- Hydrophobic/Hydrophillic
- Ionic Bonds
- Hydrogen Bonds
- Disulphide
Quaternary Structure
Association between two or more proteins called subunits
Nucleic Acids
They are large molecules made up of carbon, hydrogen, oxygen, nitrogen and phosphorus.
The monomers of nucleic acids are known nucleotides.
Responsible in storing and transmitting genetic information
How are Nucleotides bonded together? What do they form?
When nucleotides join together in a chain, what do they form?
Nucleotides bond together through condensation reactions between their phosphate group at the 5’ carbon of one nucleotide and the 3’ carbon of the pentose sugar and this forms a phosphodiester bond. Water is produced. This bonding forms a strong sugar-phosphate backbone
What is a Nucelotide made up of?
- A pentose monosaccharide
- A phosphate group
- A nitrogenous base (adenine, thymine, guanine or cytosine in DNA)
Deoxyribose
One less oxygen than the ribose sugar
Pyrimidines
These are nitrogenous bases which have only one carbon ring.
Thymine and Cytosine
Cats under the pyramids
Purine
These are bases with double carbon ringed structures.
These are Guanine and Adenine
1) What is the Structure of DNA
2) How is DNA’s shape formed
3) Anti-Parallel strands
4) Complementary Base Pairings (What makes A only bind to T)
1) Two strands of polynucleotides that join together through 5’ to 3’ phosphodiester bonds with the phosphate group at 5’ and the Hydroxyl group at 3’. The polynucleotides in DNA are held together through hydrogen bonds between bases on each polynucleotide.
2) DNA’s shape is formed because a purine base always bonds to a pyrimidine base and the hydrogen bonds in between them maintain a fixed distance between the polynucleotide chains. Since a pyrimidine has one carbon ring and a purine has two carbon rings, by these two always interacting together, they maintain a fixed distance between the polynucleotide chains.
3) The two strands in DNA are anti parallel because they run in opposing directions. One 5’ to 3’ sugar phosphate backbone exists and the other is flipped, running the opposing direction
4) Adenine only binds to thymine because if the hydrogen bonds they form. Adenine and Thymine form two hydrogen bonds and Cytosine and Guanine form three hydrogen bonds
Why does A-T and C-G
Because of Adenine bonding to thymine producing 2 hydrogen bonds and Cytosine bonding to Guanine producing 3 hydrogen bonds
How is the distance between the two DNA polynucleotide backbone maintained
Pyrimidines only bonding to Purines
RNA (Function and Use)
Ribose nucleic acid. All genetic information in the nucleolus is too long to leave the nucleus.
RNA is a copy of a section of the DNA molecule.
It directs protein synthesis
Thymine is Replaced by Uracil which is also a Pyrimidine
Semi Conservative Replication
1) DNA molecule unwinds then separates into two strands as DNA Helicase breaks the hydrogen bonds holding the two polynucleotides together
2) Free DNA Nucleotides will then pair with their complementary bases, and a sugar phosphate backbone will be formed as phosphodiester bonds form, catalysed by DNA Polymerase
Forms 2 DNA molecule which has one old and one new strand
Mutation in Semi Conservative Replication
Occurs as a result of incorrect matching of bases in the new strand. Leads to a change in sequence of the bases
Genetic Code is Degenerate, Universal and Non-Overlapping
Universal - Same Codons code for the same amino acids in every organism
Degenerate - Multiple codons can code for the same amino acids and this protects against mutations
Non-Overlapping - Nucleotides can’t code for more than one amino acid
Transcription (1st step in protein synthesis)
- DNA is in the nuclear envelope and is too large to leave the nucleus. To get around this, the base sequence of genes in the DNA needs to be transported to the ribosomes where protein synthesis occurs
- DNA molecule unwinds then unzips by the use of DNA helicase and hydrogen bonds broken. It just opens up
- Only one of the two strands codes for the protein to be synthesised. This is the sense strand that runs from 5’ to 3’. The other is the antisense strand that runs from 3’ to 5’ that acts as the template strand in which the RNA molecule will form complementary bases for
- Free RNA nucleotides will form base pairs with the anti-sense strand and then phosphodiester bonds form between the nucleotides using the enzyme RNA Polymerase
- Once the RNA molecule is done forming its bonds, it leaves the DNA molecule and is now called mRNA. This mRNA molecule leaves the nucleus through a nuclear pore and then travels to the ribosome for the next step
Translation (2nd Step in Protein Synthesis)
-mRNA molecule binds to a specific part of the ribosome where it is held in place while it is translated to a sequence of amino acids
-tRNA molecules bring amino acids. They have an anticodon for the RNA and they also have an amino acid attaches on top of it.
- Two tRNA molecules bind to the RNA molecule and there is a peptide bond formed between the amino acids on them. it is catalysed by the enzyme peptidyl transferase
- Once there is a peptide bond between the amino acids, the tRNA molecule is released
- The ribosome then moves along the RNA molecule and more and more tRNA molecules attach and the chain of amino acids grow, forming the primary structure of the protein
- The protein then folds further into its secondary and tertiary structure
- It may undergo further modifications in the golgi apparatus
- Note that many Ribosomes can attach onto the mRNA molecule so many polypeptides can be synthesised at once
ATP
How does it release energy (reaction)
Why is ATP not a good long term store
Adenine Triphosphate is a nucleotide made up of adenine (nitrogenous base), ribose (sugar) and three phosphate groups.
It releases energy through the breaking of the last phosphate group and when the phosphate group forms other bonds. Water is involved in the removal of the phosphate group
ATP + H20 —> ADP + Phosphate + Energy
ATP is hydrolysed to produce Adenine Diphosphate, the phosphate ion and energy
ATP is not a good long term store because of the instability of the last phosphate group and the weak bond holding it on
How ATP is created
Fats and Carbohydrates are long term stores of energy. When they are broken down through cellular respiration, it’s allows a phosphate molecule to attach onto an ADP molecule, turning it into an ATP molecule this process is called phosphorylation, where a phosphate group is added to ADP to form ATP
Properties of ATP
- Small and can move in and out of cells easily
- Not a suitable long term of energy storage due to the phosphate group attached to the end being highly unstable.
- Water Soluble. It allows metabolic reactions that use ATP to occur in aqueous environments
- Easily Regenerating. It is generated through cellular respiration
Benedict’s test for Reducing Sugars (Qualitative Test)
Based on the fact that all monosaccharides and some disaccharides donate electrons. Benedict’s reagent is made up of Copper(II) sulfate and is an alkaline solution.
- Blend into water if not solid and mix with water.
- Add equal amount of Benedict’s Reagent
- Place it in a water bath for 5 Minutes
- Reducing sugars would cause a change in colour from blue to brick red as the Copper(II)+ ions gain an electron
It is a qualitative test because depending on the amount of reducing sugars present, the harshness of the blue or brick red precipitate will fluctuate depending on the concentration of the reducing sugars present
Benedict’s test for Non-Reducing Sugars
- Non reducing sugars can’t donate electrons
- Sucrose would have to be boiled in dilute HCl to be hydrolysed and then produce glucose and fructose, two monosaccharides. These would then cause a brick red colour to be formed
Iodine Test for Starch
- A few drops of iodine dissolved in potassium iodide solution is mixed with the sample that may contain starch
- If the sample changes colour from yellow/brown to purple/black, there is a positive result
What is Sucrose made up of
alpha glucose and fructose
